Lake Arrowhead Microbial Genomics #LAMG16: Day 4 and Random Thoughts

Only three talks on the last day. First up was Jordan Parker “Microbiome Course-based Undergraduate Research Experiences (CUREs) Benefit Students and Faculty”. Great talk about how we need to move from cookbook labs to discovery-based research, talked about the “I Microbiologist” textbook. The challenge is to scale research to class-sized groups. She described the competency-based lab curriculum at UCLA which sounds like a great chance for students to get an authentic research experience. Their microbial diversity course has both a metagenomics and a culture-based component, focuses on rhizosphere which has tractable questions the students can ask. Talked about the need for cheap outsourced sequencing and GUI-based analysis tools. Showed some cool examples from the program as well as assessment data highlighting learning gains of students in the program.

Next was Matthew Olm “Identical Bacterial Populations Colonize Premature Infant Gut, Skin, and Oral Microbiomes and Exhibit Different in situ Growth Rates”. Started by showing how “weird” and important the early microbiome is. Describing a very detailed study of two premature infants, trying to understand early colonization and the development of body-site specificity. Found the same strains for many species on various body sites, but that replications rates vary between sites… but replication doesn’t correspond with abundance.

Last talk was Sean Conlan, “Plasmid Dynamics During Long-term Colonization with blaKPC-Positive Klebsiella pneumonia“. Started by painting a fairly bleak picture of the spread of this bug. Trying to understand transmission and long-term carriage. A large and variable number of plasmids between isolates, clearly an important part of the population structure and pathogenesis. Talked us through a detailed study of a couple of patients over time, and how the plasmids changed.

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A few overall random thoughts from my 3rd Lake Arrowhead meeting:

-There is clearly an emphasis on “return to culture”, the days of 16S stamp collecting appear to be coming to an end. Many people used 16S or metagenomic data as a starting place, and then did cool experiments to test hypotheses coming from the surveys. Which is awesome.

-As costs have continued to fall, the amount of genomes that people sequence for a single experiment has skyrocketed. Where 10 genomes used to be a big deal for comparative analysis, a few studies sequenced over 1000 genomes for SNP analysis. And then of course the JGI presented an analysis of 9000 (!) metagenomes.

-More people are considering, and talking about, Citizen Science and public outreach as components of their projects. Which is awesome and I hope this trend continues. There is so much awesome and exciting research in this area that I think we have to work harder to convey that to the public (but without the snake oil and overselling that has also become popular).

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David Coil

David Coil is a Project Scientist in the lab of Jonathan Eisen at UC Davis. David works at the intersection between research, education, and outreach in the areas of the microbiology of the built environment, microbial ecology, and bacterial genomics. Twitter